Pathway Analysis

calcTNullFast | Compute Null T Distribution for Each Gene |

calcTStatFast | Compute T-Statistics and Corresponding P-Values |

calculate.GSEA | Calculate 2-sided statistics based on the GSEA algorithm |

calculate.NGSk | Calculate NGSk (NTk-like) statistics with gene label... |

calculatePathwayStatistics | Calculate the NTk and NEk statistics |

estimateNumPerm | Compute the Number of Unique Permutations for a Phenotype... |

getPathwayStatistics | Give the statistics for the probe sets in a pathway |

getPathwayStatistics.NGSk | Give the statistics for the probe sets in a pathway |

importGeneSets | Import gene sets stored in GMT, GMX, GRP, and XML file... |

MuscleExample | Subset of Inflammatory Myopathy Dataset to Demonstrate... |

rankPathways | Summarizes Top Pathways from Pathway Analyses |

rankPathways.NGSk | Summarizes Top Pathways from One of the Pathway Analyses |

runSigPathway | Perform pathway analysis |

selectGeneSets | Select gene sets to be analyzed in pathway analysis |

writeSigPathway | Write results of pathway analysis to HTML format |

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